1
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Koncz M, Stirling T, Hadj Mehdi H, Méhi O, Eszenyi B, Asbóth A, Apjok G, Tóth Á, Orosz L, Vásárhelyi BM, Ari E, Daruka L, Polgár TF, Schneider G, Zalokh SA, Számel M, Fekete G, Bohár B, Nagy Varga K, Visnyovszki Á, Székely E, Licker MS, Izmendi O, Costache C, Gajic I, Lukovic B, Molnár S, Szőcs-Gazdi UO, Bozai C, Indreas M, Kristóf K, Van der Henst C, Breine A, Pál C, Papp B, Kintses B. Genomic surveillance as a scalable framework for precision phage therapy against antibiotic-resistant pathogens. Cell 2024; 187:5901-5918.e28. [PMID: 39332413 DOI: 10.1016/j.cell.2024.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 05/15/2024] [Accepted: 09/04/2024] [Indexed: 09/29/2024]
Abstract
Phage therapy is gaining increasing interest in the fight against critically antibiotic-resistant nosocomial pathogens. However, the narrow host range of bacteriophages hampers the development of broadly effective phage therapeutics and demands precision approaches. Here, we combine large-scale phylogeographic analysis with high-throughput phage typing to guide the development of precision phage cocktails targeting carbapenem-resistant Acinetobacter baumannii, a top-priority pathogen. Our analysis reveals that a few strain types dominate infections in each world region, with their geographical distribution remaining stable within 6 years. As we demonstrate in Eastern Europe, this spatiotemporal distribution enables preemptive preparation of region-specific phage collections that target most local infections. Finally, we showcase the efficacy of phage cocktails against prevalent strain types using in vitro and animal infection models. Ultimately, genomic surveillance identifies patients benefiting from the same phages across geographical scales, thus providing a scalable framework for precision phage therapy.
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Affiliation(s)
- Mihály Koncz
- Synthetic and Systems Biology Unit, Institute of Biochemistry, National Laboratory of Biotechnology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary; HCEMM-BRC Translational Microbiology Research Group, Budapesti út 9, 6728 Szeged, Hungary
| | - Tamás Stirling
- Synthetic and Systems Biology Unit, Institute of Biochemistry, National Laboratory of Biotechnology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary; HCEMM-BRC Translational Microbiology Research Group, Budapesti út 9, 6728 Szeged, Hungary; Doctoral School of Biology, University of Szeged, Dugonics tér 13, 6720 Szeged, Hungary
| | - Hiba Hadj Mehdi
- Synthetic and Systems Biology Unit, Institute of Biochemistry, National Laboratory of Biotechnology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary; HCEMM-BRC Translational Microbiology Research Group, Budapesti út 9, 6728 Szeged, Hungary; Doctoral School of Biology, University of Szeged, Dugonics tér 13, 6720 Szeged, Hungary
| | - Orsolya Méhi
- Synthetic and Systems Biology Unit, Institute of Biochemistry, National Laboratory of Biotechnology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary
| | - Bálint Eszenyi
- Synthetic and Systems Biology Unit, Institute of Biochemistry, National Laboratory of Biotechnology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary
| | - András Asbóth
- Synthetic and Systems Biology Unit, Institute of Biochemistry, National Laboratory of Biotechnology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary; HCEMM-BRC Translational Microbiology Research Group, Budapesti út 9, 6728 Szeged, Hungary; Department of Genetics, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/C, 1117 Budapest, Hungary
| | - Gábor Apjok
- Synthetic and Systems Biology Unit, Institute of Biochemistry, National Laboratory of Biotechnology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary
| | - Ákos Tóth
- National Center for Public Health and Pharmacy, Albert Flórián út 2-6, 1097 Budapest, Hungary
| | - László Orosz
- Department of Medical Microbiology, University of Szeged, Szent-Györgyi Albert Medical School, Dom tér 10, 6720 Szeged, Hungary
| | - Bálint Márk Vásárhelyi
- Synthetic and Systems Biology Unit, Institute of Biochemistry, National Laboratory of Biotechnology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary
| | - Eszter Ari
- Synthetic and Systems Biology Unit, Institute of Biochemistry, National Laboratory of Biotechnology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary; Department of Genetics, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/C, 1117 Budapest, Hungary; HCEMM-BRC Metabolic Systems Biology Group, Temesvári Krt. 62, 6726 Szeged, Hungary
| | - Lejla Daruka
- Synthetic and Systems Biology Unit, Institute of Biochemistry, National Laboratory of Biotechnology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary
| | - Tamás Ferenc Polgár
- Institute of Biophysics, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary; Theoretical Medicine Doctoral School, University of Szeged, Dugonics tér 13, 6720 Szeged, Hungary
| | - György Schneider
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
| | - Sif Aldin Zalokh
- Synthetic and Systems Biology Unit, Institute of Biochemistry, National Laboratory of Biotechnology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary
| | - Mónika Számel
- Synthetic and Systems Biology Unit, Institute of Biochemistry, National Laboratory of Biotechnology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary
| | - Gergely Fekete
- Synthetic and Systems Biology Unit, Institute of Biochemistry, National Laboratory of Biotechnology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary; HCEMM-BRC Metabolic Systems Biology Group, Temesvári Krt. 62, 6726 Szeged, Hungary
| | - Balázs Bohár
- Synthetic and Systems Biology Unit, Institute of Biochemistry, National Laboratory of Biotechnology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary; Faculty of Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, 10th Floor Commonwealth Building Hammersmith Campus, Du Cane Road, London W12 0NN, UK
| | - Karolina Nagy Varga
- Synthetic and Systems Biology Unit, Institute of Biochemistry, National Laboratory of Biotechnology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary
| | - Ádám Visnyovszki
- South-Pest Central Hospital National Institute of Hematology and Infectious Diseases, Nagyvárad tér 1, 1097 Budapest, Hungary; Doctoral School of Interdisciplinary Medical Sciences, University of Szeged, Dugonics tér 13, 6720 Szeged, Hungary
| | - Edit Székely
- George Emil Palade University of Medicine, Pharmacy, Science and Technology of Targu Mures, Str. Gheorghe Marinescu 38, 540142 Targu Mures, Romania; County Emergency Clinical Hospital of Targu Mures, Str. Dr. Gh. Marinescu 50, 540136 Targu Mures, Romania
| | - Monica-Sorina Licker
- Microbiology Department, Multidisciplinary Research Center on Antimicrobial Resistance, "Victor Babes" University of Medicine and Pharmacy, Str. Eftimie Murgu 2, 300041 Timisoara, Romania; Microbiology Laboratory, "Pius Branzeu" Emergency Clinical County Hospital, Str. Liviu Rebreanu 156, 300723 Timisoara, Romania
| | - Oana Izmendi
- Microbiology Department, Multidisciplinary Research Center on Antimicrobial Resistance, "Victor Babes" University of Medicine and Pharmacy, Str. Eftimie Murgu 2, 300041 Timisoara, Romania; Microbiology Laboratory, "Pius Branzeu" Emergency Clinical County Hospital, Str. Liviu Rebreanu 156, 300723 Timisoara, Romania; Doctoral School, "Victor Babes" University of Medicine and Pharmacy, Str. Eftimie Murgu 2, 300041 Timisoara, Romania
| | - Carmen Costache
- Department of Microbiology, University of Medicine and Pharmacy "Iuliu Hatieganu" Cluj-Napoca, Str. Victor Babes 8, 400347 Cluj-Napoca, Romania
| | - Ina Gajic
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Dr Subotica 8, 11000 Belgrade, Serbia
| | - Bojana Lukovic
- Academy of Applied Studies Belgrade, College of Health Sciences, Bulevar Zorana Djindjica 152a, Belgrade, Serbia
| | - Szabolcs Molnár
- Emergency County Hospital Miercurea-Ciuc, Str. Doctor Dénes László 2, 530173 Miercurea Ciuc, Romania
| | | | - Csilla Bozai
- County Emergency Hospital Satu Mare, Str. Ravensburg 1-3, 440192 Satu Mare, Romania
| | - Marina Indreas
- Bacau County Emergency Hospital, Str. Haret Spiru 2-4, 600114 Bacau, Romania
| | - Katalin Kristóf
- Institute of Laboratory Medicine, Semmelweis University, Üllői út 78/b, 1083 Budapest, Hungary
| | - Charles Van der Henst
- Microbial Resistance and Drug Discovery, VIB-VUB Center for Structural Biology, VIB, Flanders Institute for Biotechnology, Pleinlaan 2, Building E-3, 1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Pleinlaan 2, Elsene, 1050 Brussels, Belgium
| | - Anke Breine
- Microbial Resistance and Drug Discovery, VIB-VUB Center for Structural Biology, VIB, Flanders Institute for Biotechnology, Pleinlaan 2, Building E-3, 1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Pleinlaan 2, Elsene, 1050 Brussels, Belgium
| | - Csaba Pál
- Synthetic and Systems Biology Unit, Institute of Biochemistry, National Laboratory of Biotechnology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary
| | - Balázs Papp
- Synthetic and Systems Biology Unit, Institute of Biochemistry, National Laboratory of Biotechnology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary; HCEMM-BRC Metabolic Systems Biology Group, Temesvári Krt. 62, 6726 Szeged, Hungary; National Laboratory for Health Security, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary.
| | - Bálint Kintses
- Synthetic and Systems Biology Unit, Institute of Biochemistry, National Laboratory of Biotechnology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726 Szeged, Hungary; HCEMM-BRC Translational Microbiology Research Group, Budapesti út 9, 6728 Szeged, Hungary.
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2
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Webb JR, Andersson P, Sim E, Zahedi A, Donald A, Hoang T, Watt AE, Agius JE, Donato CM, Cummins ML, Zulfiqar T, Nghiem S, Lin C, Menouhos D, Leong LEX, Baird R, Kennedy K, Cooley L, Speers D, Lim CK, de Ligt J, Ferdinand A, Glass K, Kirk MD, Djordjevic SP, Sloggett C, Horan K, Seemann T, Sintchenko V, Jennison AV, Howden BP. Implementing a national programme of pathogen genomics for public health: the Australian Pathogen Genomics Program (AusPathoGen). THE LANCET. MICROBE 2024:100969. [PMID: 39389079 DOI: 10.1016/j.lanmic.2024.100969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 07/19/2024] [Accepted: 07/31/2024] [Indexed: 10/12/2024]
Abstract
Delivering large-scale routine pathogen genomics surveillance for public health is of considerable interest, although translational research models that promote national-level implementation are not well defined. We describe the development and deployment of the Australian Pathogen Genomics Program (AusPathoGen), a comprehensive national partnership between academia, public health laboratories, and public health agencies that commenced in January, 2021. Successfully establishing and delivering a national programme requires inclusive and transparent collaboration between stakeholders, defined and clear focus on public health priorities, and support for strengthening national genomics capacity. Major enablers for delivering such a programme include technical solutions for data integration and analysis, such as the genomics surveillance platform AusTrakka, standard bioinformatic analysis methods, and national ethics and data sharing agreements that promote nationally integrated surveillance systems. Training of public health officials to interpret and act on genomic data is crucial, and evaluation and cost-effectiveness programmes will provide a benchmark and evidence for sustainable investment in genomics nationally and globally.
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Affiliation(s)
- Jessica R Webb
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Centre for Pathogen Genomics, University of Melbourne, Melbourne, VIC, Australia
| | - Patiyan Andersson
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Centre for Pathogen Genomics, University of Melbourne, Melbourne, VIC, Australia
| | - Eby Sim
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW, Australia; Centre for Infectious Diseases and Microbiology-Public Health, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, NSW, Australia
| | - Alireza Zahedi
- Public and Environmental Health, Pathology Queensland Queensland Health, Brisbane, QLD, Australia
| | - Angela Donald
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Tuyet Hoang
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Centre for Pathogen Genomics, University of Melbourne, Melbourne, VIC, Australia
| | - Anne E Watt
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Jessica E Agius
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW, Australia; Centre for Infectious Diseases and Microbiology-Public Health, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, NSW, Australia
| | - Celeste M Donato
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Centre for Pathogen Genomics, University of Melbourne, Melbourne, VIC, Australia
| | - Max L Cummins
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, NSW, Australia; Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Sydney, NSW, Australia
| | - Tehzeeb Zulfiqar
- National Centre for Epidemiology and Population Health, The Australian National University, Canberra, ACT, Australia
| | - Son Nghiem
- National Centre for Epidemiology and Population Health, The Australian National University, Canberra, ACT, Australia
| | - Chantel Lin
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Centre for Pathogen Genomics, University of Melbourne, Melbourne, VIC, Australia
| | | | | | - Rob Baird
- Territory Pathology, Royal Darwin Hospital, Darwin, NT, Australia
| | - Karina Kennedy
- Department of Clinical Microbiology and Infectious Diseases, Canberra Health Services, Australian National University Medical School of Medicine and Psychology, Canberra, ACT, Australia
| | - Louise Cooley
- Department of Microbiology and Infectious Diseases, Royal Hobart Hospital, Tasmania, Australia; Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, TAS, Australia
| | - David Speers
- Department of Microbiology, PathWest Laboratory Medicine WA, Queen Elizabeth II Medical Centre, Perth, WA, Australia
| | - Chuan Kok Lim
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Joep de Ligt
- Institute of Environmental Science and Research, Kenepuru, Porirua, New Zealand
| | - Angeline Ferdinand
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Centre for Pathogen Genomics, University of Melbourne, Melbourne, VIC, Australia; Centre for Health Policy, School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
| | - Katie Glass
- National Centre for Epidemiology and Population Health, The Australian National University, Canberra, ACT, Australia
| | - Martyn D Kirk
- National Centre for Epidemiology and Population Health, The Australian National University, Canberra, ACT, Australia
| | - Steven P Djordjevic
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, NSW, Australia; Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Sydney, NSW, Australia
| | - Clare Sloggett
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Kristy Horan
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Torsten Seemann
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Centre for Pathogen Genomics, University of Melbourne, Melbourne, VIC, Australia
| | - Vitali Sintchenko
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW, Australia; Centre for Infectious Diseases and Microbiology-Public Health, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, NSW, Australia
| | - Amy V Jennison
- Public and Environmental Health, Pathology Queensland Queensland Health, Brisbane, QLD, Australia
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Centre for Pathogen Genomics, University of Melbourne, Melbourne, VIC, Australia; Department of Infectious Diseases, Austin Health, Heidelberg, VIC, Australia.
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3
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Getchell M, Wulandari S, de Alwis R, Agoramurthy S, Khoo YK, Mak TM, Moe L, Stona AC, Pang J, Momin MHFHA, Amir A, Andalucia LR, Azzam G, Chin S, Chookajorn T, Arunkumar G, Hung DT, Ikram A, Jha R, Karlsson EA, Le Thi MQ, Mahasirimongkol S, Malavige GN, Manning JE, Munira SL, Trung NV, Nisar I, Qadri F, Qamar FN, Robinson MT, Saloma CP, Setk S, Shirin T, Tan LV, Dizon TJR, Thayan R, Thu HM, Tissera H, Xangsayarath P, Zaini Z, Lim JCW, Maurer-Stroh S, Smith GJD, Wang LF, Pronyk P. Pathogen genomic surveillance status among lower resource settings in Asia. Nat Microbiol 2024; 9:2738-2747. [PMID: 39317773 PMCID: PMC11445059 DOI: 10.1038/s41564-024-01809-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 08/14/2024] [Indexed: 09/26/2024]
Abstract
Asia remains vulnerable to new and emerging infectious diseases. Understanding how to improve next generation sequencing (NGS) use in pathogen surveillance is an urgent priority for regional health security. Here we developed a pathogen genomic surveillance assessment framework to assess capacity in low-resource settings in South and Southeast Asia. Data collected between June 2022 and March 2023 from 42 institutions in 13 countries showed pathogen genomics capacity exists, but use is limited and under-resourced. All countries had NGS capacity and seven countries had strategic plans integrating pathogen genomics into wider surveillance efforts. Several pathogens were prioritized for human surveillance, but NGS application to environmental and human-animal interface surveillance was limited. Barriers to NGS implementation include reliance on external funding, supply chain challenges, trained personnel shortages and limited quality assurance mechanisms. Coordinated efforts are required to support national planning, address capacity gaps, enhance quality assurance and facilitate data sharing for decision making.
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Affiliation(s)
- Marya Getchell
- Programme in Health Services and Systems Research, Duke-NUS Medical School, Singapore, Singapore
| | - Suci Wulandari
- Centre for Outbreak Preparedness, Duke-NUS Medical School, Singapore, Singapore
| | - Ruklanthi de Alwis
- Centre for Outbreak Preparedness, Duke-NUS Medical School, Singapore, Singapore.
- SingHealth Duke-NUS Global Health Institute, Singapore, Singapore.
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore.
| | - Shreya Agoramurthy
- Centre for Outbreak Preparedness, Duke-NUS Medical School, Singapore, Singapore
| | - Yoong Khean Khoo
- Centre for Outbreak Preparedness, Duke-NUS Medical School, Singapore, Singapore
- Centre of Regulatory Excellence, Duke-NUS Medical School, Singapore, Singapore
| | - Tze-Minn Mak
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - La Moe
- Centre for Outbreak Preparedness, Duke-NUS Medical School, Singapore, Singapore
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Anne-Claire Stona
- Centre for Outbreak Preparedness, Duke-NUS Medical School, Singapore, Singapore
- Centre of Regulatory Excellence, Duke-NUS Medical School, Singapore, Singapore
| | - Junxiong Pang
- Centre for Outbreak Preparedness, Duke-NUS Medical School, Singapore, Singapore
- SingHealth Duke-NUS Global Health Institute, Singapore, Singapore
| | | | | | | | - Ghows Azzam
- Malaysia Genome and Vaccine Institute (MGVI), Selangor, Malaysia
- School of Biological Sciences, Universiti Sains Malaysia, Gelugor, Penang, Malaysia
| | - Savuth Chin
- National Institute of Public Health, Phnom Penh, Cambodia
| | - Thanat Chookajorn
- Mahidol University, Nakhon Pathom, Thailand
- Umeå University, Umeå, Sweden
| | | | | | - Aamer Ikram
- National Institute of Health (NIH), Islamabad, Pakistan
| | - Runa Jha
- National Public Health Laboratory, Kathmandu, Nepal
| | | | - Mai Quynh Le Thi
- National Institute of Hygien and Epidemiology (NIHE), Nha Trang, Vietnam
| | | | | | - Jessica E Manning
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Phnom Penh, Cambodia
| | | | | | | | - Firdausi Qadri
- International Centre for Diarrhoeal Disease Research (icddr,b), Dhaka, Bangladesh
| | | | - Matthew T Robinson
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Quai Fa Ngum, Vientiane, Laos
- Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Cynthia P Saloma
- Philippine Genome Center, University of the Philippines, Luzon, Philippines
| | - Swe Setk
- National Health Laboratory, Department of Medical Service, Ministry of Health, Yangon, Myanmar
| | - Tahmina Shirin
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka, Bangladesh
| | - Le Van Tan
- Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam
| | | | | | - Hlaing Myat Thu
- Department of Medical Research, Ministry of Health, Yangon, Myanmar
| | | | | | - Zainun Zaini
- Department of Laboratory Services, Ministry of Health, Bandar Seri Begawan, Brunei
| | - John C W Lim
- SingHealth Duke-NUS Global Health Institute, Singapore, Singapore
- Centre of Regulatory Excellence, Duke-NUS Medical School, Singapore, Singapore
| | - Sebastian Maurer-Stroh
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Infectious Diseases Labs, Agency for Science, Technology and Research, Singapore, Singapore
- Yong Loo Lin School of Medicine and Department of Biology, National University of Singapore, Singapore, Singapore
| | - Gavin J D Smith
- Centre for Outbreak Preparedness, Duke-NUS Medical School, Singapore, Singapore
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
- SingHealth Duke-NUS Global Health Institute, Singapore, Singapore
| | - Paul Pronyk
- Centre for Outbreak Preparedness, Duke-NUS Medical School, Singapore, Singapore
- SingHealth Duke-NUS Global Health Institute, Singapore, Singapore
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4
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Faure AJ, Martí-Aranda A, Hidalgo-Carcedo C, Beltran A, Schmiedel JM, Lehner B. The genetic architecture of protein stability. Nature 2024:10.1038/s41586-024-07966-0. [PMID: 39322666 DOI: 10.1038/s41586-024-07966-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 08/20/2024] [Indexed: 09/27/2024]
Abstract
There are more ways to synthesize a 100-amino acid (aa) protein (20100) than there are atoms in the universe. Only a very small fraction of such a vast sequence space can ever be experimentally or computationally surveyed. Deep neural networks are increasingly being used to navigate high-dimensional sequence spaces1. However, these models are extremely complicated. Here, by experimentally sampling from sequence spaces larger than 1010, we show that the genetic architecture of at least some proteins is remarkably simple, allowing accurate genetic prediction in high-dimensional sequence spaces with fully interpretable energy models. These models capture the nonlinear relationships between free energies and phenotypes but otherwise consist of additive free energy changes with a small contribution from pairwise energetic couplings. These energetic couplings are sparse and associated with structural contacts and backbone proximity. Our results indicate that protein genetics is actually both rather simple and intelligible.
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Affiliation(s)
- Andre J Faure
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- ALLOX, Barcelona, Spain.
| | - Aina Martí-Aranda
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Cristina Hidalgo-Carcedo
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Antoni Beltran
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Jörn M Schmiedel
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- factorize.bio, Berlin, Germany
| | - Ben Lehner
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
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5
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Park JS, Akarapipad P, Chen FE, Shao F, Mostafa H, Hsieh K, Wang TH. Digitized Kinetic Analysis Enhances Genotyping Capacity of CRISPR-Based Biosensing. ACS NANO 2024; 18:18058-18070. [PMID: 38922290 DOI: 10.1021/acsnano.4c05312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/27/2024]
Abstract
CRISPR/Cas systems have been widely employed for nucleic acid biosensing and have been further advanced for mutation detection by virtue of the sequence specificity of crRNA. However, existing CRISPR-based genotyping methods are limited by the mismatch tolerance of Cas effectors, necessitating a comprehensive screening of crRNAs to effectively distinguish between wild-type and point-mutated sequences. To circumvent the limitation of conventional CRISPR-based genotyping, here, we introduce Single-Molecule kinetic Analysis via a Real-Time digital CRISPR/Cas12a-assisted assay (SMART-dCRISPR). SMART-dCRISPR leverages the differential kinetics of the signal increase in CRISPR/Cas systems, which is modulated by the complementarity between crRNA and the target sequence. It employs single-molecule digital measurements to discern mutations based on kinetic profiles that could otherwise be obscured by variations in the target concentrations. We applied SMART-dCRISPR to genotype notable mutations in SARS-CoV-2, point mutation (K417N) and deletion (69/70DEL), successfully distinguishing wild-type, Omicron BA.1, and Omicron BA.2 SARS-CoV-2 strains from clinical nasopharyngeal/nasal swab samples. Additionally, we introduced a portable digital real-time sensing device to streamline SMART-dCRISPR and enhance its practicality for point-of-care settings. The combination of a rapid and sensitive isothermal CRISPR-based assay with single-molecule kinetic analysis in a portable format significantly enhances the versatility of CRISPR-based nucleic acid biosensing and genotyping.
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Affiliation(s)
- Joon Soo Park
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Patarajarin Akarapipad
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Fan-En Chen
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Fangchi Shao
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Heba Mostafa
- Department of Pathology, Johns Hopkins University, School of Medicine, Baltimore, Maryland 21287, United States
| | - Kuangwen Hsieh
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Tza-Huei Wang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States
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6
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Dosbaa A, Guilbaud R, Yusti AMF, Ferré VM, Charpentier C, Descamps D, Le Hingrat Q, Coppée R. RSV-GenoScan: An automated pipeline for whole-genome human respiratory syncytial virus (RSV) sequence analysis. J Virol Methods 2024; 327:114938. [PMID: 38588779 DOI: 10.1016/j.jviromet.2024.114938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 03/17/2024] [Accepted: 04/05/2024] [Indexed: 04/10/2024]
Abstract
BACKGROUND Advances in high-throughput sequencing (HTS) technologies and reductions in sequencing costs have revolutionised the study of genomics and molecular biology by making whole-genome sequencing (WGS) accessible to many laboratories. However, the analysis of WGS data requires significant computational effort, which is the major drawback in implementing WGS as a routine laboratory technique. OBJECTIVE Automated pipelines have been developed to overcome this issue, but they do not exist for all organisms. This is the case for human respiratory syncytial virus (RSV), which is a leading cause of lower respiratory tract infections in infants, the elderly, and immunocompromised adults. RESULTS We present RSV-GenoScan, a fast and easy-to-use pipeline for WGS analysis of RSV generated by HTS on Illumina or Nanopore platforms. RSV-GenoScan automates the WGS analysis steps directly from the raw sequence data. The pipeline filters the sequence data, maps the reads to the RSV reference genomes, generates a consensus sequence, identifies the RSV subgroup, and lists amino acid mutations, insertions and deletions in the F and G viral genes. This enables the rapid identification of mutations in these coding genes that are known to confer resistance to monoclonal antibodies. AVAILABILITY RSV-GenoScan is freely available at https://github.com/AlexandreD-bio/RSV-GenoScan.
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Affiliation(s)
- Alexandre Dosbaa
- Université Paris Cité and Université Sorbonne Paris Nord, Inserm, IAME, Paris F-75018, France
| | - Romane Guilbaud
- Université Paris Cité and Université Sorbonne Paris Nord, Inserm, IAME, Paris F-75018, France; Service de Virologie, AP-HP, Hôpital Bichat - Claude Bernard, Paris F-75018, France
| | - Anna-Maria Franco Yusti
- Université Paris Cité and Université Sorbonne Paris Nord, Inserm, IAME, Paris F-75018, France
| | - Valentine Marie Ferré
- Université Paris Cité and Université Sorbonne Paris Nord, Inserm, IAME, Paris F-75018, France; Service de Virologie, AP-HP, Hôpital Bichat - Claude Bernard, Paris F-75018, France
| | - Charlotte Charpentier
- Université Paris Cité and Université Sorbonne Paris Nord, Inserm, IAME, Paris F-75018, France; Service de Virologie, AP-HP, Hôpital Bichat - Claude Bernard, Paris F-75018, France
| | - Diane Descamps
- Université Paris Cité and Université Sorbonne Paris Nord, Inserm, IAME, Paris F-75018, France; Service de Virologie, AP-HP, Hôpital Bichat - Claude Bernard, Paris F-75018, France
| | - Quentin Le Hingrat
- Université Paris Cité and Université Sorbonne Paris Nord, Inserm, IAME, Paris F-75018, France; Service de Virologie, AP-HP, Hôpital Bichat - Claude Bernard, Paris F-75018, France
| | - Romain Coppée
- Université Paris Cité and Université Sorbonne Paris Nord, Inserm, IAME, Paris F-75018, France.
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7
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Wong W, Schaffner SF, Thwing J, Seck MC, Gomis J, Diedhiou Y, Sy N, Ndiop M, Ba F, Diallo I, Sene D, Diallo MA, Ndiaye YD, Sy M, Sene A, Sow D, Dieye B, Tine A, Ribado J, Suresh J, Lee A, Battle KE, Proctor JL, Bever CA, MacInnis B, Ndiaye D, Hartl DL, Wirth DF, Volkman SK. Evaluating the performance of Plasmodium falciparum genetic metrics for inferring National Malaria Control Programme reported incidence in Senegal. Malar J 2024; 23:68. [PMID: 38443939 PMCID: PMC10916253 DOI: 10.1186/s12936-024-04897-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 02/29/2024] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND Genetic surveillance of the Plasmodium falciparum parasite shows great promise for helping National Malaria Control Programmes (NMCPs) assess parasite transmission. Genetic metrics such as the frequency of polygenomic (multiple strain) infections, genetic clones, and the complexity of infection (COI, number of strains per infection) are correlated with transmission intensity. However, despite these correlations, it is unclear whether genetic metrics alone are sufficient to estimate clinical incidence. METHODS This study examined parasites from 3147 clinical infections sampled between the years 2012-2020 through passive case detection (PCD) across 16 clinic sites spread throughout Senegal. Samples were genotyped with a 24 single nucleotide polymorphism (SNP) molecular barcode that detects parasite strains, distinguishes polygenomic (multiple strain) from monogenomic (single strain) infections, and identifies clonal infections. To determine whether genetic signals can predict incidence, a series of Poisson generalized linear mixed-effects models were constructed to predict the incidence level at each clinical site from a set of genetic metrics designed to measure parasite clonality, superinfection, and co-transmission rates. RESULTS Model-predicted incidence was compared with the reported standard incidence data determined by the NMCP for each clinic and found that parasite genetic metrics generally correlated with reported incidence, with departures from expected values at very low annual incidence (< 10/1000/annual [‰]). CONCLUSIONS When transmission is greater than 10 cases per 1000 annual parasite incidence (annual incidence > 10‰), parasite genetics can be used to accurately infer incidence and is consistent with superinfection-based hypotheses of malaria transmission. When transmission was < 10‰, many of the correlations between parasite genetics and incidence were reversed, which may reflect the disproportionate impact of importation and focal transmission on parasite genetics when local transmission levels are low.
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Affiliation(s)
- Wesley Wong
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Stephen F Schaffner
- Infectious Disease and Microbiome Program, The Broad Institute, Cambridge, MA, USA
| | - Julie Thwing
- Malaria Branch, Division of Parasitic Diseases and Malaria, Global Health Center, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Mame Cheikh Seck
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Jules Gomis
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Younouss Diedhiou
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Ngayo Sy
- Section de Lutte Anti-Parasitaire (SLAP) Clinic, Thies, Senegal
| | - Medoune Ndiop
- Programme National de Lutte contre le Paludisme (PNLP), Dakar, Senegal
| | - Fatou Ba
- Programme National de Lutte contre le Paludisme (PNLP), Dakar, Senegal
| | - Ibrahima Diallo
- Programme National de Lutte contre le Paludisme (PNLP), Dakar, Senegal
| | - Doudou Sene
- Programme National de Lutte contre le Paludisme (PNLP), Dakar, Senegal
| | - Mamadou Alpha Diallo
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Yaye Die Ndiaye
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Mouhamad Sy
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Aita Sene
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Djiby Sow
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Baba Dieye
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Abdoulaye Tine
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Jessica Ribado
- Institute for Disease Modeling at the Bill and Melinda Gates Foundation, Seattle, WA, USA
| | - Joshua Suresh
- Institute for Disease Modeling at the Bill and Melinda Gates Foundation, Seattle, WA, USA
| | - Albert Lee
- Institute for Disease Modeling at the Bill and Melinda Gates Foundation, Seattle, WA, USA
| | - Katherine E Battle
- Institute for Disease Modeling at the Bill and Melinda Gates Foundation, Seattle, WA, USA
| | - Joshua L Proctor
- Institute for Disease Modeling at the Bill and Melinda Gates Foundation, Seattle, WA, USA
| | - Caitlin A Bever
- Institute for Disease Modeling at the Bill and Melinda Gates Foundation, Seattle, WA, USA
| | - Bronwyn MacInnis
- Infectious Disease and Microbiome Program, The Broad Institute, Cambridge, MA, USA
| | - Daouda Ndiaye
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Daniel L Hartl
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Dyann F Wirth
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Infectious Disease and Microbiome Program, The Broad Institute, Cambridge, MA, USA
| | - Sarah K Volkman
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
- Infectious Disease and Microbiome Program, The Broad Institute, Cambridge, MA, USA.
- College of Natural, Behavioral, and Health Sciences, Simmons University, Boston, MA, USA.
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8
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Drake KO, Boyd O, Franceschi VB, Colquhoun RM, Ellaby NAF, Volz EM. Phylogenomic early warning signals for SARS-CoV-2 epidemic waves. EBioMedicine 2024; 100:104939. [PMID: 38194742 PMCID: PMC10792554 DOI: 10.1016/j.ebiom.2023.104939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 01/11/2024] Open
Abstract
BACKGROUND Epidemic waves of coronavirus disease 2019 (COVID-19) infections have often been associated with the emergence of novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants. Rapid detection of growing genomic variants can therefore serve as a predictor of future waves, enabling timely implementation of countermeasures such as non-pharmaceutical interventions (social distancing), additional vaccination (booster campaigns), or healthcare capacity adjustments. The large amount of SARS-CoV-2 genomic sequence data produced during the pandemic has provided a unique opportunity to explore the utility of these data for generating early warning signals (EWS). METHODS We developed an analytical pipeline (Transmission Fitness Polymorphism Scanner - designated in an R package mrc-ide/tfpscanner) for systematically exploring all clades within a SARS-CoV-2 virus phylogeny to detect variants showing unusually high growth rates. We investigated the use of these cluster growth rates as the basis for a variety of statistical time series to use as leading indicators for the epidemic waves in the UK during the pandemic between August 2020 and March 2022. We also compared the performance of these phylogeny-derived leading indicators with a range of non-phylogeny-derived leading indicators. Our experiments simulated data generation and real-time analysis. FINDINGS Using phylogenomic analysis, we identified leading indicators that would have generated EWS ahead of significant increases in COVID-19 hospitalisations in the UK between August 2020 and March 2022. Our results also show that EWS lead time is sensitive to the threshold set for the number of false positive (FP) EWS. It is often possible to generate longer EWS lead times if more FP EWS are tolerated. On the basis of maximising lead time and minimising the number of FP EWS, the best performing leading indicators that we identified, amongst a set of 1.4 million, were the maximum logistic growth rate (LGR) amongst clusters of the dominant Pango lineage and the mean simple LGR across a broader set of clusters. In the case of the former, the time between the EWS and wave inflection points (a conservative measure of wave start dates) for the seven waves ranged between a 20-day lead time and a 7-day lag, with a mean lead time of 5.4 days. The maximum number of FP EWS generated prior to a true positive (TP) EWS was two and this only occurred for two of the seven waves in the period. The mean simple LGR amongst a broader set of clusters also performed well in terms of lead time but with slightly more FP EWS. INTERPRETATION As a result of the significant surveillance effort during the pandemic, early detection of SARS-CoV-2 variants of concern Alpha, Delta, and Omicron provided some of the first examples where timely detection and characterisation of pathogen variants has been used to tailor public health response. The success of our method in generating early warning signals based on phylogenomic analysis for SARS-CoV-2 in the UK may make it a worthwhile addition to existing surveillance strategies. In addition, the method may be translatable to other countries and/or regions, and to other pathogens with large-scale and rapid genomic surveillance. FUNDING This research was funded in whole, or in part, by the Wellcome Trust (220885_Z_20_Z). For the purpose of open access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. KOD, OB, VBF and EMV acknowledge funding from the MRC Centre for Global Infectious Disease Analysis (reference MR/X020258/1), jointly funded by the UK Medical Research Council (MRC) and the UK Foreign, Commonwealth & Development Office (FCDO), under the MRC/FCDO Concordat agreement and is also part of the EDCTP2 programme supported by the European Union. RMC acknowledges funding from the Wellcome Trust Collaborators Award (206298/Z/17/Z).
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Affiliation(s)
- Kieran O Drake
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom.
| | - Olivia Boyd
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
| | - Vinicius B Franceschi
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
| | - Rachel M Colquhoun
- Institute of Evolutionary Biology, Ashworth Laboratories, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Erik M Volz
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
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9
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Sirichoat A, Kaewprasert O, Hinwan Y, Faksri K. Phenotypic drug-susceptibility profiles and genetic analysis based on whole-genome sequencing of Mycobacterium avium complex isolates in Thailand. PLoS One 2023; 18:e0294677. [PMID: 37992075 PMCID: PMC10664917 DOI: 10.1371/journal.pone.0294677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 10/31/2023] [Indexed: 11/24/2023] Open
Abstract
Mycobacterium avium complex (MAC) infections are a significant clinical challenge. Determining drug-susceptibility profiles and the genetic basis of drug resistance is crucial for guiding effective treatment strategies. This study aimed to determine the drug-susceptibility profiles of MAC clinical isolates and to investigate the genetic basis conferring drug resistance using whole-genome sequencing (WGS) analysis. Drug-susceptibility profiles based on minimum inhibitory concentration (MIC) assays were determined for 38 MAC clinical isolates (12 Mycobacterium avium and 26 Mycobacterium intracellulare). Mutations associated with drug resistance were identified through genome analysis of these isolates, and their phylogenetic relationships were also examined. Drug resistance, based on MIC values, was most commonly observed for moxifloxacin (81.6%), followed by linezolid (78.9%), clarithromycin (44.7%) and amikacin (36.8%). We identified specific mutations associated with resistance to amikacin. These include the rrs mutation at C464T in amikacin intermediate-resistance M. avium, and two mutations at T250A and G1453T in amikacin non-susceptible M. intracellulare. Mutations in rrl at A2058G, A2059C and A2059G were potentially linked to clarithromycin resistance. MAC clinical isolates not susceptible to linezolid exhibited mutations in rplC at G237C and C459T, as well as two rplD mutations at G443A and A489G. GyrB substitution Thr521Ala (T521A) was identified in moxifloxacin non-susceptible isolates, which may contribute to this resistance. A phylogeny of our MAC isolates revealed high levels of genetic diversity. Our findings suggest that the standard treatment regimen for MAC infections using moxifloxacin, linezolid, clarithromycin and amikacin may be driving development of resistance, potentially due to specific mutations. The combination of phenotypic and genotypic susceptibility testing can be valuable in guiding the clinical use of drugs for the treatment of MAC infections.
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Affiliation(s)
- Auttawit Sirichoat
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand
| | - Orawee Kaewprasert
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand
| | - Yothin Hinwan
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand
| | - Kiatichai Faksri
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand
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10
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Hill V, Githinji G, Vogels CBF, Bento AI, Chaguza C, Carrington CVF, Grubaugh ND. Toward a global virus genomic surveillance network. Cell Host Microbe 2023; 31:861-873. [PMID: 36921604 PMCID: PMC9986120 DOI: 10.1016/j.chom.2023.03.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
The COVID-19 pandemic galvanized the field of virus genomic surveillance, demonstrating its utility for public health. Now, we must harness the momentum that led to increased infrastructure, training, and political will to build a sustainable global genomic surveillance network for other epidemic and endemic viruses. We suggest a generalizable modular sequencing framework wherein users can easily switch between virus targets to maximize cost-effectiveness and maintain readiness for new threats. We also highlight challenges associated with genomic surveillance and when global inequalities persist. We propose solutions to mitigate some of these issues, including training and multilateral partnerships. Exploring alternatives to clinical sequencing can also reduce the cost of surveillance programs. Finally, we discuss how establishing genomic surveillance would aid control programs and potentially provide a warning system for outbreaks, using a global respiratory virus (RSV), an arbovirus (dengue virus), and a regional zoonotic virus (Lassa virus) as examples.
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Affiliation(s)
- Verity Hill
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.
| | - George Githinji
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya; Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya
| | - Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA; Yale Institute for Global Health, Yale University, New Haven, CT, USA
| | - Ana I Bento
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health-Bloomington, Bloomington, IN, USA; The Rockefeller Foundation, New York, NY, USA
| | - Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA; Yale Institute for Global Health, Yale University, New Haven, CT, USA
| | - Christine V F Carrington
- Department of Preclinical Sciences, The University of the West Indies, St. Augustine Campus, St. Augustine, Trinidad and Tobago
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA; Yale Institute for Global Health, Yale University, New Haven, CT, USA; Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA; Public Health Modeling Unit, Yale School of Public Health, New Haven, CT, USA.
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11
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Tosta S, Moreno K, Schuab G, Fonseca V, Segovia FMC, Kashima S, Elias MC, Sampaio SC, Ciccozzi M, Alcantara LCJ, Slavov SN, Lourenço J, Cella E, Giovanetti M. Global SARS-CoV-2 genomic surveillance: What we have learned (so far). INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 108:105405. [PMID: 36681102 PMCID: PMC9847326 DOI: 10.1016/j.meegid.2023.105405] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/13/2023] [Accepted: 01/17/2023] [Indexed: 01/20/2023]
Abstract
The COVID-19 pandemic has brought significant challenges for genomic surveillance strategies in public health systems worldwide. During the past thirty-four months, many countries faced several epidemic waves of SARS-CoV-2 infections, driven mainly by the emergence and spread of novel variants. In that line, genomic surveillance has been a crucial toolkit to study the real-time SARS-CoV-2 evolution, for the assessment and optimization of novel diagnostic assays, and to improve the efficacy of existing vaccines. During the pandemic, the identification of emerging lineages carrying lineage-specific mutations (particularly those in the Receptor Binding domain) showed how these mutations might significantly impact viral transmissibility, protection from reinfection and vaccination. So far, an unprecedented number of SARS-CoV-2 viral genomes has been released in public databases (i.e., GISAID, and NCBI), achieving 14 million genome sequences available as of early-November 2022. In the present review, we summarise the global landscape of SARS-CoV-2 during the first thirty-four months of viral circulation and evolution. It demonstrates the urgency and importance of sustained investment in genomic surveillance strategies to timely identify the emergence of any potential viral pathogen or associated variants, which in turn is key to epidemic and pandemic preparedness.
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Affiliation(s)
- Stephane Tosta
- Interunit Postgraduate Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Keldenn Moreno
- Interunit Postgraduate Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Gabriel Schuab
- Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil; Laboratório de Flavivirus, Instituto Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Vagner Fonseca
- Organização Pan-Americana da Saúde/Organização Mundial da Saúde, Brasília, Distrito Federal, Brazil.
| | | | - Simone Kashima
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo,Brazil
| | | | | | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Italy
| | - Luiz Carlos Junior Alcantara
- Interunit Postgraduate Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil; Laboratório de Flavivirus, Instituto Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Svetoslav Nanev Slavov
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo,Brazil; Butantan Institute, São Paulo, Brazil
| | - José Lourenço
- BioISI (Biosystems and Integrative Sciences Institute), Faculdade de Ciências da Universidade de Lisboa, Lisboa,Portugal
| | - Eleonora Cella
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32827, USA.
| | - Marta Giovanetti
- Interunit Postgraduate Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil; Laboratório de Flavivirus, Instituto Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil; Department of Science and Technology for Humans and the Environment, University of Campus Bio-Medico di Roma, Rome, Italy.
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12
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Du H, Dong E, Badr HS, Petrone ME, Grubaugh ND, Gardner LM. Incorporating variant frequencies data into short-term forecasting for COVID-19 cases and deaths in the USA: a deep learning approach. EBioMedicine 2023; 89:104482. [PMID: 36821889 PMCID: PMC9943054 DOI: 10.1016/j.ebiom.2023.104482] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 01/30/2023] [Accepted: 02/02/2023] [Indexed: 02/24/2023] Open
Abstract
BACKGROUND Since the US reported its first COVID-19 case on January 21, 2020, the science community has been applying various techniques to forecast incident cases and deaths. To date, providing an accurate and robust forecast at a high spatial resolution has proved challenging, even in the short term. METHOD Here we present a novel multi-stage deep learning model to forecast the number of COVID-19 cases and deaths for each US state at a weekly level for a forecast horizon of 1-4 weeks. The model is heavily data driven, and relies on epidemiological, mobility, survey, climate, demographic, and SARS-CoV-2 variant frequencies data. We implement a rigorous and robust evaluation of our model-specifically we report on weekly performance over a one-year period based on multiple error metrics, and explicitly assess how our model performance varies over space, chronological time, and different outbreak phases. FINDINGS The proposed model is shown to consistently outperform the CDC ensemble model for all evaluation metrics in multiple spatiotemporal settings, especially for the longer-term (3 and 4 weeks ahead) forecast horizon. Our case study also highlights the potential value of variant frequencies data for use in short-term forecasting to identify forthcoming surges driven by new variants. INTERPRETATION Based on our findings, the proposed forecasting framework improves upon the available state-of-the-art forecasting tools currently used to support public health decision making with respect to COVID-19 risk. FUNDING This work was funded the NSF Rapid Response Research (RAPID) grant Award ID 2108526 and the CDC Contract #75D30120C09570.
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Affiliation(s)
- Hongru Du
- Center for Systems Science and Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA; Department of Civil and Systems Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Ensheng Dong
- Center for Systems Science and Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA; Department of Civil and Systems Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Hamada S Badr
- Center for Systems Science and Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA; Department of Civil and Systems Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA; Department of Earth and Planetary Sciences, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Mary E Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA; Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06510, USA
| | - Lauren M Gardner
- Center for Systems Science and Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA; Department of Civil and Systems Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA.
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